He is being investigated in connection with massive fraud at the privately owned Kabul Bank and the printing of unauthorised amounts of currency.
Earlier, it emerged Mr Fitrat had fled Afghanistan for the US - he said his life was in danger for exposing fraud.
He said the Afghan government had hindered his attempts to investigate corruption.
Afghanistan's Deputy Attorney General Rahmatullah Nazari said he would ask the US embassy and Interpol for help in securing Mr Fitrat's arrest.
"He will be brought here to face the judiciary. We will follow him," he told the BBC.
"There are some serious charges against him. He needs to answer all of them.''
Continue reading the main story 2004: Kabul Bank founded by international poker player, Sherkhan FarnoodSeptember 2010: Kabul Bank taken over by the central bank after a run on the bank amid fears of its collapseFebruary 2011: Abdul Qadeer Fitrat, central bank governor, tells BBC those involved in bank's woes should be prosecutedFebruary 2011: An IMF report recommends the bank be put in receivershipApril 2011: Mr Fitrat, names in parliament prominent Afghan figures in connection with the Kabul Bank scandalMay 2011: Report by anti-corruption office shows $467m (?290m) of outstanding loans were made without appropriate collateralCharges made against Mr Fitrat include that he financially mismanaged the bank, sabotaged the country's economy, ignored advice from other government institutions and did not adequately observe private banks.The US - where Mr Fitrat has residency - does not have an extradition treaty with Afghanistan. He has said he has no plans to return to Afghanistan.
The embezzlement at Kabul Bank, Afghanistan's largest private bank, almost led to its collapse last year after it was discovered that hundreds of millions of dollars had gone missing.
The bank handles up to 80% of the government payroll, including salaries for policemen and teachers.
In April, Mr Fitrat accused several key Afghan officials - including President Hamid Karzai's brother and Vice-President Qasim Fahim - of being involved. Both deny the charges.
Then on Monday, he told reporters he had had to leave the country after receiving information that his life was in danger from "credible sources".
'Difficult job'Mr Fitrat alleges that the central government did not assist him in his investigations or provide any help in recovering the bank's assets.
Continue reading the main story Bilal Sarwary KabulRelations have been frosty between the West and Kabul over the issue of corruption. The case of Kabul Bank was closely followed by the international community and the Afghan people - most were hoping all those involved would be prosecuted.
Resolving the issue is crucial in ensuring aid money continues to flow into Afghanistan. The International Monetary Fund wants the Afghan government to wind down the bank before it releases a new assistance programme.
Billions of dollars in international aid hinge on that programme.
"During [the] last 10 months during the Kabul Bank crisis, I continuously pressed for the creation of a special prosecution, for the creation of a special tribunal to investigate and prosecute those who were involved in Kabul Bank's fraud," he told the BBC."I did not receive any information that there is a credible plan to prosecute, to investigate and prosecute these individuals. The high political authorities of the country were responsible [for blocking] these efforts," he alleged.
President Karzai has said Afghanistan lacks the necessary banking experience to oversee the central institution and has blamed foreign advisers for the crisis.
He has also pledged to ensure that those responsible are subject to criminal investigations.
The UK Department for International Development said Mr Fitrat's resignation was "regrettable", and that he had done "a difficult job handling a complex set of challenges".
"It is absolutely critical that the government of Afghanistan chooses a good quality replacement with thorough knowledge of the banking sector," it said in a statement.
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